Variant report

Variant	rs6539268
Chromosome Location	chr12:106789757-106789758
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 168 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10047654	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10444532	0.86[EUR][1000 genomes]
rs10507211	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs10746059	0.80[ASN][1000 genomes]
rs10746060	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778464	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10778465	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778468	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778469	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778470	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778471	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778473	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778474	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778475	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778476	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778477	0.88[ASN][1000 genomes]
rs10778478	1.00[ASN][1000 genomes]
rs10778480	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778481	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861571	1.00[CHB][hapmap]
rs10861577	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs10861578	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs10861579	0.86[EUR][1000 genomes]
rs10861580	0.92[ASN][1000 genomes]
rs10861581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861582	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861583	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs10861585	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861586	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861587	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs10861588	1.00[CHB][hapmap]
rs10861589	0.92[ASN][1000 genomes]
rs10861590	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10861591	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10861592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861593	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861594	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861595	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861597	1.00[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861598	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861599	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861604	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861605	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861608	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861609	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861613	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11112933	1.00[CHB][hapmap]
rs11112940	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11112942	0.81[ASN][1000 genomes]
rs11112943	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11112945	0.86[EUR][1000 genomes]
rs11112948	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11112949	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11112951	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs11112952	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs11112953	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11112957	0.92[ASN][1000 genomes]
rs11112961	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112979	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112980	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112986	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112990	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112991	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112992	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112993	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112995	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11113003	0.88[ASN][1000 genomes]
rs11113004	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11113009	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1134577	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11609315	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11611176	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11611252	1.00[ASN][1000 genomes]
rs11611815	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11615682	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11835357	1.00[ASN][1000 genomes]
rs11835362	0.88[ASN][1000 genomes]
rs12298876	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12305705	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309708	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12309758	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12312915	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322877	0.89[ASN][1000 genomes]
rs12370430	1.00[CHB][hapmap]
rs12422988	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12423068	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12424952	1.00[CHB][hapmap]
rs12425459	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17038414	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17218490	1.00[CHB][hapmap]
rs17221107	0.86[AFR][1000 genomes]
rs17284674	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17285274	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs1921952	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2141774	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141775	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2243455	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2264759	0.85[AFR][1000 genomes]
rs2374606	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2374610	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28669886	0.81[ASN][1000 genomes]
rs2888888	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2900499	0.86[EUR][1000 genomes]
rs2900500	0.86[EUR][1000 genomes]
rs34955444	0.80[ASN][1000 genomes]
rs3851631	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851632	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851633	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625578	0.85[EUR][1000 genomes]
rs55678155	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55689816	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58297001	0.81[ASN][1000 genomes]
rs58767490	0.81[ASN][1000 genomes]
rs60224628	0.81[ASN][1000 genomes]
rs60635749	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61940334	0.81[ASN][1000 genomes]
rs61940335	0.81[ASN][1000 genomes]
rs61940342	0.81[ASN][1000 genomes]
rs61941917	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941918	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941920	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941921	0.88[ASN][1000 genomes]
rs61941922	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61941943	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941944	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61943670	0.86[EUR][1000 genomes]
rs61943672	0.80[ASN][1000 genomes]
rs61943690	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61943693	0.84[ASN][1000 genomes]
rs61943694	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539269	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6539270	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6539271	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67911933	0.92[ASN][1000 genomes]
rs67966244	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7132744	0.85[EUR][1000 genomes]
rs7132971	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7134615	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134881	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7135054	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7136098	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7137445	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7139139	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139249	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7297873	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7298062	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7298462	0.80[ASN][1000 genomes]
rs7303873	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306012	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7306277	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7306326	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7308541	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309020	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310703	0.80[ASN][1000 genomes]
rs7311957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7313040	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7315549	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7961133	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7963213	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7965520	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7969743	1.00[ASN][1000 genomes]
rs7971581	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976305	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106752400-106791600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:106753000-106791600	Weak transcription	Esophagus	oesophagus
3	chr12:106753000-106793200	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:106753000-106811800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:106753000-106815400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:106755400-106796400	Weak transcription	Spleen	Spleen
7	chr12:106764000-106821000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:106764400-106811800	Weak transcription	HUVEC	blood vessel
9	chr12:106765000-106790600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:106767200-106808600	Weak transcription	NHDF-Ad	bronchial
11	chr12:106773000-106828000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:106773200-106789800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:106773200-106808600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:106774400-106834000	Weak transcription	Small Intestine	intestine
15	chr12:106774600-106791600	Weak transcription	Fetal Thymus	thymus
16	chr12:106774600-106819000	Weak transcription	Right Ventricle	heart
17	chr12:106774800-106811800	Weak transcription	NHEK	skin
18	chr12:106776200-106790400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:106776800-106793400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:106776800-106821800	Weak transcription	Brain Angular Gyrus	brain
21	chr12:106777200-106791600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:106777200-106791600	Weak transcription	Aorta	Aorta
23	chr12:106777400-106808200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:106779600-106821800	Weak transcription	Brain Substantia Nigra	brain
25	chr12:106781200-106799600	Weak transcription	Osteobl	bone
26	chr12:106782000-106791200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:106782000-106810000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:106783600-106818800	Weak transcription	Fetal Heart	heart
29	chr12:106784600-106791400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:106784800-106790600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:106784800-106791400	Strong transcription	Primary T cells from cord blood	blood
32	chr12:106784800-106791800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:106784800-106791800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:106784800-106791800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr12:106786000-106789800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:106786400-106790800	Strong transcription	Dnd41	blood
37	chr12:106786400-106791800	Strong transcription	Liver	Liver
38	chr12:106786400-106792000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:106786600-106789800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:106786600-106790000	Strong transcription	Lung	lung
41	chr12:106786600-106790200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:106786600-106790200	Strong transcription	Fetal Intestine Large	intestine
43	chr12:106786600-106790200	Strong transcription	Fetal Lung	lung
44	chr12:106786600-106790200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr12:106786600-106790400	Strong transcription	Adipose Nuclei	Adipose
46	chr12:106786600-106790600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:106786600-106790600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:106786600-106790600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:106786600-106790800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:106786600-106791600	Strong transcription	Primary monocytes fromperipheralblood	blood

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